Effect of manipulating recombination rates on response to selection in livestock breeding programs.

Mara Battagin,Anne-Michelle Faux,John M Hickey,Susan E Johnston,Gregor Gorjanc

doi:10.1186/s12711-016-0221-1

Mara Battagin, Anne-Michelle Faux + Show 3 more

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https://doi.org/10.1186/s12711-016-0221-1

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Abstract

BackgroundIn this work, we performed simulations to explore the potential of manipulating recombination rates to increase response to selection in livestock breeding programs.MethodsWe carried out ten replicates of several scenarios that followed a common overall structure but differed in the average rate of recombination along the genome (expressed as the length of a chromosome in Morgan), the genetic architecture of the trait under selection, and the selection intensity under truncation selection (expressed as the proportion of males selected). Recombination rates were defined by simulating nine different chromosome lengths: 0.10, 0.25, 0.50, 1, 2, 5, 10, 15 and 20 Morgan, respectively. One Morgan was considered to be the typical chromosome length for current livestock species. The genetic architecture was defined by the number of quantitative trait variants (QTV) that affected the trait under selection. Either a large (10,000) or a small (1000 or 500) number of QTV was simulated. Finally, the proportions of males selected under truncation selection as sires for the next generation were equal to 1.2, 2.4, 5, or 10 %.ResultsIncreasing recombination rate increased the overall response to selection and decreased the loss of genetic variance. The difference in cumulative response between low and high recombination rates increased over generations. At low recombination rates, cumulative response to selection tended to asymptote sooner and the genetic variance was completely eroded. If the trait under selection was affected by few QTV, differences between low and high recombination rates still existed, but the selection limit was reached at all rates of recombination.ConclusionsHigher recombination rates can enhance the efficiency of breeding programs to turn genetic variation into response to selection. However, to increase response to selection significantly, the recombination rate would need to be increased 10- or 20-fold. The biological feasibility and consequences of such large increases in recombination rates are unknown.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0221-1) contains supplementary material, which is available to authorized users.

Highlights

In this work, we performed simulations to explore the potential of manipulating recombination rates to increase response to selection in livestock breeding programs
The differences in response to selection and genetic and genic variances between low and high recombination rates increased over generations
If the trait under selection was affected by a few quantitative trait variants (QTV), differences in response to selection between low and high recombination rates still existed, but the selection limit was reached for all rates of recombination

Summary

Introduction

We performed simulations to explore the potential of manipulating recombination rates to increase response to selection in livestock breeding programs. The Battagin et al Genet Sel Evol (2016) 48:44 upper limits of its impact on selection response are likely to be reached in the near future since accuracy asymptote, cost constraints and generation interval cannot be reduced further without adopting new reproduction techniques These constraints suggest that manipulating the amount of genetic variation that is available for selection will become an important goal for breeders in attempts to further increase response to selection. In the simulation study of Gorjanc et al [5], the Bulmer effect was estimated by subtracting the additive genetic variance (variance of breeding values) from the additive genic variance (variance of breeding values assuming that QTV are completely unlinked) These authors reported additive genic and genetic variances of 0.28 in an unselected base population and 0.22 and 0.16, respectively, after ten generations of random mating and ten generations of selection. The generation of new combinations of alleles is constrained by their arrangement on the chromosomes in any given generation and, the QTV cannot be selected upon in an independent manner

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